[R] lattice plot formatting: pch, abbreviation and labels
Duncan Mackay
dulcalma at bigpond.com
Wed Apr 30 01:31:21 CEST 2014
Forgot to cc to list
Hi Luigi
Our emails are apparently crossing
What you are doing is referencing down ONLY to the stimulation level and not
the stimulation level + productivity level required for each of the N and P groups
notch<-0.3
stripplot(
copy ~ factor(positivity)|factor(stimulation, levels = c("Unst.",
"ESAT6","CFP10","Rv3615c", "Rv2654","Rv3879", "Rv3873","PHA")),
my.data,
group = positivity,
hor=F,
layout = c(8,1),
scales = list(x = list(at = c(1,2), labels = c("N","P"))),
jitter.data=TRUE, pch=c(16,1), col="black",
ylab=expression(bold("Copy")),
xlab=expression(bold("Stimulation")),
main="Plot",
par.settings = list(strip.background=list(col="white")),
par.strip.text=list(font=2),
key = key.plot,
panel = function(x, y, ...)
{
pnl = panel.number()
for (i in 1:2){
datme<-subset(datmeA, positivity==i-1)
w<-i+k
panel.segments(x0 = X[w], y0 = datme[datme[,2]== levels(datme[,2])[pnl],"copy"],
x1 = X[w+1], y1 = datme[datme[,2]== levels(datme[,2])[pnl],"copy"],lwd = 2, col = "black")
k=k+1
panel.stripplot(x,y, ...)
panel.stripplot(x,y, ...)
}
}
)
for (i in 1:2){
datme<-subset(datmeA, positivity==i-1)
w<-i+k
panel.segments(x0 = X[w], y0 = datme[datme[,2]== levels(datme[,2])[pnl],"copy"],
x1 = X[w+1], y1 = datme[datme[,2]== levels(datme[,2])[pnl],"copy"],lwd = 2, col = "black")
k=k+1
panel.stripplot(x,y, ...)
the more lattice way is
notch<-0.3
stripplot(
copy ~ factor(positivity)|factor(stimulation, levels = c("Unst.",
"ESAT6","CFP10","Rv3615c", "Rv2654","Rv3879", "Rv3873","PHA")),
my.data,
group = positivity,
hor=F,
layout = c(8,1),
scales = list(x = list(at = c(1,2), labels = c("N","P"))),
jitter.data=TRUE, pch=c(16,1), col="black",
ylab=expression(bold("Copy")),
xlab=expression(bold("Stimulation")),
main="Plot",
par.settings = list(strip.background=list(col="white")),
par.strip.text=list(font=2),
key = key.plot,
panel = panel.superpose,
panel.groups = function(x, y, group.number, ...) {
panel.segments(x0= x-notch, x1=x+notch, y0=mean(y), y1=mean(y), lty = c(1:2)[group.number],
lwd=c(2:1)[group.number], col = c(1:2)[group.number])
panel.stripplot(x,y, ...)
}
)
Duncan
-----Original Message-----
From: Luigi Marongiu [mailto:marongiu.luigi at gmail.com]
Sent: Wednesday, 30 April 2014 02:44
To: Duncan Mackay
Subject: Re: [R] lattice plot formatting: pch, abbreviation and labels
Dear Duncan,
I think the solution is close by. I can now plot the segments directly
with stripplot using a vector containing the required positions; the
only problem is to generate 4 consecutive indeces using two nested
loops -- using the subtraction of the index and a number I obtained
the duplication of the values, as you can see in the second example.
Many thanks,
Luigi
X<-c(0.7, 1.3, 1.7, 2.3)
stripplot(
copy ~ factor(positivity)|factor(stimulation, levels = c("Unst.",
"ESAT6","CFP10","Rv3615c", "Rv2654","Rv3879", "Rv3873","PHA")),
my.data,
group = positivity,
hor=F,
layout = c(8,1),
scales = list(x = list(at = c(1,2), labels = c("N","P"))),
jitter.data=TRUE, pch=c(16,1), col="black",
ylab=expression(bold("Copy")),
xlab=expression(bold("Stimulation")),
main="Plot",
par.settings = list(strip.background=list(col="white")),
par.strip.text=list(font=2),
key = key.plot,
panel = function(x, y, ...)
{
pnl = panel.number()
for (i in 1:2){
datme<-subset(datmeA, positivity==i-1)
k<-i-1
for (j in 1:2)
{
panel.segments(x0 = X[k+j], y0 = datme[datme[,2]==
levels(datme[,2])[pnl],"copy"],
x1 = X[k+j+1], y1 =
datme[datme[,2]== levels(datme[,2])[pnl],"copy"],lwd = 2, col =
c("magenta","grey"))
}
panel.stripplot(x,y, ...)
}
}
)
#### this approach gives duplications:
notch<-0.3
stripplot(
copy ~ factor(positivity)|factor(stimulation, levels = c("Unst.",
"ESAT6","CFP10","Rv3615c", "Rv2654","Rv3879", "Rv3873","PHA")),
my.data,
group = positivity,
hor=F,
layout = c(8,1),
scales = list(x = list(at = c(1,2), labels = c("N","P"))),
jitter.data=TRUE, pch=c(16,1), col="black",
ylab=expression(bold("Copy")),
xlab=expression(bold("Stimulation")),
main="Plot",
par.settings = list(strip.background=list(col="white")),
par.strip.text=list(font=2),
key = key.plot,
panel = function(x, y, ...)
{
pnl = panel.number()
for (i in 1:2){
datme<-subset(datmeA, positivity==i-1)
k<-i-1
for (j in 1:2)
{
panel.segments(x0 = j-notch, y0 =
datme[datme[,2]== levels(datme[,2])[pnl],"copy"],
x1 = j+notch, y1 =
datme[datme[,2]== levels(datme[,2])[pnl],"copy"],lwd = 2, col =
c("magenta","grey"))
}
panel.stripplot(x,y, ...)
}
}
)
On Tue, Apr 29, 2014 at 10:26 AM, Duncan Mackay <dulcalma at bigpond.com> wrote:
> Hi Luigi
>
> Only minor changes needed.
>
> When you go back to a normal xyplot the rules of ratio variables apply the x-axis default in your case something like pretty(range(x)
> So the x-axis limits range from 0-1
> and the panel limits therefore are 0-1 +/- 4%
> With strip stripplot being categorical the limits are for values 1 and 2 so the top value for 2 is not being shown
> (easily seen with str(xyplot object))
>
> You missed out the assigning of groups to the segments.
> You could do this by a for loop of 1:2 or by using groups/panel.groups.
> I have not got the time to dig out the code to do it at the moment.
>
> xyplot(copy ~ positivity|stimulation, data = my.data,
> group = factor(positivity),
> as.table = TRUE,
> layout = c(8,1),
> xlim = c(-1,2),
> scales = list(x = list(at = c(0,1),
> labels = c("N","P"),
> rot = 0)),
> jitter.data=TRUE,
> pch=c(16,1),
> col="black",
> ylab=expression(bold("Copy")),
> xlab=expression(bold("Stimulation")),
> main="Plot",
> par.settings = list(strip.background=list(col="white")),
> par.strip.text=list(font=2),
> key = list(space="top",
> columns=2,
> text=list(c("Positive", "Negative"), col="black"),
> points=list(pch=c(16,1), col="black")),
> panel = function(x, y,...){
> pnl = panel.number()
> #panel.abline(h = datmeA[datmeA[,2]== levels(datmeA[,2])[pnl],"ratio"], col = c("red","black"), lty=3)
> #for (j in 1:2){
> # with(subset(datmeA, (positivity == j-1 & stimulation == levels(datmeA$stimulation)[pnl])),
> # panel.abline(h = copy, lwd = 1, col = c("red","black")[j], lty = 1) )
> for (j in 1:2){
> panel.segments(x0 = (j-1)-0.25, y0 = datmeA[datmeA[,2]== levels(datmeA[,2])[pnl],"copy"], # amend to copy
> x1 = (j-1)+0.25, y1 = datmeA[datmeA[,2]== levels(datmeA[,2])[pnl],"copy"],
> lwd = 2, col = c("magenta","grey")[j])
> }
>
> panel.stripplot(x,y, ...)
> }
> )
> If you wanted full N P then
>
> scales = list(x = list(at = c(0,1),
> alternating = F,
> labels = c("Negative","Positive"),
> rot = 90)), # rot = 0 if labels as before
>
> Duncan
>
> -----Original Message-----
> From: Luigi Marongiu [mailto:marongiu.luigi at gmail.com]
> Sent: Tuesday, 29 April 2014 04:34
> To: Duncan Mackay
> Subject: Re: [R] lattice plot formatting: pch, abbreviation and labels
>
> Dear Duncan,
> sorry to pester you again with this, but probably the solution is
> getting closer. following one of your previous tips i could write the
> xyplot synthax as you suggested:
>
> library(lattice)
> my.data<-structure(list(
> column_1 = 1:120,
> column_2 = structure(c(
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8,
> 1,2,3,4,5,6,7,8), .Label = c("Unst.", "ESAT6", "CFP10", "Rv3615c",
> "Rv2654", "Rv3879", "Rv3873", "PHA"), class = "factor"),
> column_3 = structure(c(
> 0,0,0,0,0,0,0,0,
> 0,0,0,0,0,0,0,0,
> 0,0,0,0,0,0,0,0,
> 0,0,0,0,0,0,0,0,
> 0,0,0,0,0,0,0,0,
> 0,0,0,0,0,0,0,0,
> 0,0,0,0,0,0,0,0,
> 1,1,1,1,1,1,1,1,
> 1,1,1,1,1,1,1,1,
> 1,1,1,1,1,1,1,1,
> 1,1,1,1,1,1,1,1,
> 1,1,1,1,1,1,1,1,
> 1,1,1,1,1,1,1,1,
> 1,1,1,1,1,1,1,1,
> 0,0,0,0,0,0,0,0)),
> column_4 = c(
> 192.0519108,183.6403531,53.46798757,83.60638077,69.60749873,159.4706861,256.8765622,499.2899303,
> 2170.799076,1411.349719,2759.472348,2098.973397,2164.739515,1288.676574,1611.486543,6205.229575,
> 870.7424981,465.9967135,191.8962375,864.0937485,2962.693675,1289.259137,2418.651212,7345.712517,
> 0,168.1198893,674.4342961,101.1575401,47.81596237,0,0,1420.793922,
> 142.6871331,5.466468742,291.9564635,80.73914133,73.02239621,64.47806871,144.3543635,3167.959757,
> 3164.748333,1092.634557,28733.20269,1207.87783,729.6090973,151.8706088,241.2466141,9600.963594,
> 1411.718287,12569.96285,1143.254476,6317.378481,16542.27718,79.68025792,1958.495138,7224.503437,
> 208.4382941,69.48609769,656.691151,0.499017582,7114.910926,187.6296174,41.73980805,8930.784541,
> 4.276752185,0.432300363,60.89228665,1.103924786,0.490686366,1.812993239,7.264531581,1518.610307,
> 2172.051528,595.8513744,17141.84336,589.6565971,1340.287628,117.350942,593.7034054,24043.61463,
> 0,81.83292179,1539.864321,36.41722958,8.385131047,161.7647376,65.21615696,7265.573875,
> 97.84753179,154.051827,0.613835842,10.06138851,45.04879285,176.8284258,18795.75462,30676.769,
> 5780.34957,944.2200834,2398.235596,1083.393165,2541.714557,1251.670895,1547.178549,1792.679176,
> 3067.988416,8117.210173,23676.02226,8251.937547,17360.80494,18563.61561,16941.865,31453.96708,
> 2767.493803,4796.33016,12292.93705,3864.657567,9380.673835,14886.44683,8457.88646,26050.47191)),
> .Names = c("row", "stimulation", "positivity", "copy"), row.names =
> c(NA, -120L),
> class = "data.frame")
>
> key.plot<-list(
> space="top", columns=2,
> text=list(c("Positive", "Negative"), col="black"),
> points=list(pch=c(16,1), col="black"))
>
> datmeA <- aggregate(copy ~ positivity+stimulation, my.data, median, na.rm = T)
>
>
> #### HERE IS THE IMPORTANT BIT ###
>
> xyplot(copy ~ positivity|stimulation,
> my.data,
> group = positivity,
> hor=F,
> as.table = TRUE,
> layout = c(8,1),
> scales = list(x = list(alternating = FALSE, at = c(0.2,0.8), labels
> = c("P","N"))),
> pch=c(16,1), col="black",
> ylab=expression(bold("Copy")),
> xlab=expression(bold("Stimulation")),
> main="Plot",
> par.settings = list(strip.background=list(col="white")),
> par.strip.text=list(font=2),
> key = list(space="top", columns=2, text=list(c("Positive",
> "Negative"), col="black"), points=list(pch=c(16,1), col="black")),
> panel = function(x, y, ...){
> pnl = panel.number()
> panel.segments(x0 = x-0.25, y0 = datmeA[datmeA[,2]==
> levels(datmeA[,2])[pnl],"ratio"],
> x1 = x+0.25, y1 = datmeA[datmeA[,2]==
> levels(datmeA[,2])[pnl],"ratio"],
> lwd = 2, col = c("magenta","grey"))
> panel.stripplot(x,y, ...)
> }
> )
>
> ############################
>
> beside beign less elegant than stripplot() -- there is no jittering
> and requires the positions for the labels -- there are mainly two
> problems:
> 1. the dots are too close to the margins -- I tried to use the 'at'
> argument but it did not work
> 2. the segments are replicated -- there should be a 'panel.group'
> somewhere but I obtained a lot of errors when I tried to place it.
>
> Wouldn't be easier to use the stripplot directly, using maybe a factor
> to place the segments? I tried to place the panel.function in
> stripplot but it did not work at all...
>
> stripplot(copy ~ factor(positivity)|factor(stimulation, levels =
> c("Unst.", "ESAT6","CFP10","Rv3615c", "Rv2654","Rv3879",
> "Rv3873","PHA")),
> my.data,
> group = positivity,
> hor=F,
> layout = c(8,1),
> scales = list(x = list(at = c(1,2), labels = c("N","P"))),
> jitter.data=TRUE, pch=c(16,1), col="black",
> ylab=expression(bold("Copy")),
> xlab=expression(bold("Stimulation")),
> main="Plot",
> par.settings = list(strip.background=list(col="white")),
> par.strip.text=list(font=2),
> key = list(space="top", columns=2, text=list(c("Positive",
> "Negative"), col="black"), points=list(pch=c(16,1), col="black")),
> panel = function(x, y, ...){
> pnl = panel.number()
> panel.segments(x0 = x-0.25, y0 = datmeA[datmeA[,2]==
> levels(datmeA[,2])[pnl],"ratio"],
> x1= x+0.25, y1 =
> datmeA[datmeA[,2]== levels(datmeA[,2])[pnl],"ratio"],
> lwd = 2, col = c("magenta","grey"))
> panel.stripplot(x,y, ...)
> }
> )
>
>
> Best wishes,
> Luigi
>
> On Mon, Apr 28, 2014 at 2:25 AM, Duncan Mackay <dulcalma at bigpond.com> wrote:
>> Hi Luigi
>>
>> Here are 2 ways of doing it.
>>
>> The first is a "cheats" way ie easy.
>>
>> The second is a substitute for the proper way who's code eludes me at the moment. I changed the lty on the ablines as it appears confusing and as you are bolding it seems more appropriate. A better way may be to change 1 line type.
>>
>> stripplot(copy ~ factor(positivity)|factor(stimulation, levels = c("Unst.", "ESAT6","CFP10","Rv3615c", "Rv2654","Rv3879", "Rv3873","PHA")),
>> my.data,
>> group = positivity,
>> hor=F,
>> layout = c(8,1),
>> scales = list(x = list(at = c(1,2), labels = c("N","P"))),
>> jitter.data=TRUE, pch=c(16,1), col="black",
>> ylab=expression(bold("Copy")),
>> xlab=expression(bold("Stimulation")),
>> main="Plot",
>> par.settings = list(strip.background=list(col="white")),
>> par.strip.text=list(font=2),
>> key = list(space="top",
>> columns=2,
>> text=list(c("Positive", "Negative"), col="black"),
>> points=list(pch=c(16,1), col="black")),
>> panel = function(x, y,...){
>> pnl = panel.number()
>> #panel.abline(h = datmeA[datmeA[,2]== levels(datmeA[,2])[pnl],"ratio"], col = c("red","black"), lty=3)
>>
>> panel.average(x, y, fun = mean, horizontal = F, lty = 3, col.line = c("red","black"), type = "l")
>>
>> panel.stripplot(x,y, ...)
>> }
>> )
>>
>> stripplot(copy ~ factor(positivity)|factor(stimulation, levels = c("Unst.", "ESAT6","CFP10","Rv3615c", "Rv2654","Rv3879", "Rv3873","PHA")),
>> my.data,
>> group = positivity,
>> hor=F,
>> layout = c(8,1),
>> scales = list(x = list(at = c(1,2), labels = c("N","P"))),
>> jitter.data=TRUE, pch=c(16,1), col="black",
>> ylab=expression(bold("Copy")),
>> xlab=expression(bold("Stimulation")),
>> main="Plot",
>> par.settings = list(strip.background=list(col="white")),
>> par.strip.text=list(font=2),
>> key = list(space="top",
>> columns=2,
>> text=list(c("Positive", "Negative"), col="black"),
>> points=list(pch=c(16,1), col="black")),
>> panel = function(x, y,...){
>> pnl = panel.number()
>> #panel.abline(h = datmeA[datmeA[,2]== levels(datmeA[,2])[pnl],"ratio"], col = c("red","black"), lty=3)
>> for (j in 1:2){
>> with(subset(datmeA, (positivity == j-1 & stimulation == levels(datmeA$stimulation)[pnl])),
>> panel.abline(h = copy, lwd = 1, col = c("red","black")[j], lty = 1) )
>>
>> }
>>
>> panel.stripplot(x,y, ...)
>> }
>> )
>>
>> Remember abline and panel.abline etc only take 1 line at a time so if you have more than 1 group you have 2 call it more than once
>>
>> Regards
>> Duncan
>>
>> -----Original Message-----
>> From: Luigi Marongiu [mailto:marongiu.luigi at gmail.com]
>> Sent: Monday, 28 April 2014 04:03
>> To: Duncan Mackay
>> Subject: Re: [R] lattice plot formatting: pch, abbreviation and labels
>>
>> Dear Duncan,
>> may I bother you a bit more with the same data set? I would like now
>> to add a segment corresponding to the median values, as we discussed
>> antecedently.
>> I have tried to use the code you wrote in the previous mails, but it
>> hasn't worked. First I have found the aggregate medians values and
>> assigned to datmeA, then pasted the code you wrote, but without
>> success. Would be possible to substitute the panel.abline with
>> panel.segments? but in this case how to tell lattice what are the
>> values for "N" or "P"?
>> Best wishes,
>> Luigi
>>
>> CODE::::
>> library(lattice)
>>
>> my.data<-structure(list(
>> column_1 = 1:120,
>> column_2 = structure(c(
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8,
>> 1,2,3,4,5,6,7,8), .Label = c("Unst.", "ESAT6", "CFP10", "Rv3615c",
>> "Rv2654", "Rv3879", "Rv3873", "PHA"), class = "factor"),
>> column_3 = structure(c(
>> 0,0,0,0,0,0,0,0,
>> 0,0,0,0,0,0,0,0,
>> 0,0,0,0,0,0,0,0,
>> 0,0,0,0,0,0,0,0,
>> 0,0,0,0,0,0,0,0,
>> 0,0,0,0,0,0,0,0,
>> 0,0,0,0,0,0,0,0,
>> 1,1,1,1,1,1,1,1,
>> 1,1,1,1,1,1,1,1,
>> 1,1,1,1,1,1,1,1,
>> 1,1,1,1,1,1,1,1,
>> 1,1,1,1,1,1,1,1,
>> 1,1,1,1,1,1,1,1,
>> 1,1,1,1,1,1,1,1,
>> 0,0,0,0,0,0,0,0)),
>> column_4 = c(
>> 192.0519108,183.6403531,53.46798757,83.60638077,69.60749873,159.4706861,256.8765622,499.2899303,
>> 2170.799076,1411.349719,2759.472348,2098.973397,2164.739515,1288.676574,1611.486543,6205.229575,
>> 870.7424981,465.9967135,191.8962375,864.0937485,2962.693675,1289.259137,2418.651212,7345.712517,
>> 0,168.1198893,674.4342961,101.1575401,47.81596237,0,0,1420.793922,
>> 142.6871331,5.466468742,291.9564635,80.73914133,73.02239621,64.47806871,144.3543635,3167.959757,
>> 3164.748333,1092.634557,28733.20269,1207.87783,729.6090973,151.8706088,241.2466141,9600.963594,
>> 1411.718287,12569.96285,1143.254476,6317.378481,16542.27718,79.68025792,1958.495138,7224.503437,
>> 208.4382941,69.48609769,656.691151,0.499017582,7114.910926,187.6296174,41.73980805,8930.784541,
>> 4.276752185,0.432300363,60.89228665,1.103924786,0.490686366,1.812993239,7.264531581,1518.610307,
>> 2172.051528,595.8513744,17141.84336,589.6565971,1340.287628,117.350942,593.7034054,24043.61463,
>> 0,81.83292179,1539.864321,36.41722958,8.385131047,161.7647376,65.21615696,7265.573875,
>> 97.84753179,154.051827,0.613835842,10.06138851,45.04879285,176.8284258,18795.75462,30676.769,
>> 5780.34957,944.2200834,2398.235596,1083.393165,2541.714557,1251.670895,1547.178549,1792.679176,
>> 3067.988416,8117.210173,23676.02226,8251.937547,17360.80494,18563.61561,16941.865,31453.96708,
>> 2767.493803,4796.33016,12292.93705,3864.657567,9380.673835,14886.44683,8457.88646,26050.47191)),
>> .Names = c("row", "stimulation", "positivity", "copy"), row.names =
>> c(NA, -120L),
>> class = "data.frame")
>>
>>
>> key.plot<-list(
>> space="top", columns=2,
>> text=list(c("Positive", "Negative"), col="black"),
>> points=list(pch=c(16,1), col="black"))
>>
>> datmeA <- aggregate(copy ~ positivity+stimulation, my.data, median, na.rm = T)
>>
>> stripplot(
>> copy ~ factor(positivity)|factor(stimulation,
>> levels = c("Unst.", "ESAT6","CFP10","Rv3615c", "Rv2654",
>> "Rv3879", "Rv3873","PHA")),
>> group = positivity,
>> my.data,
>> hor=F,
>> layout = c(8,1),
>> scales = list(x = list(at = c(1,2), labels = c("N","P"))),
>> jitter.data=TRUE, pch=c(16,1), col="black",
>> ylab=expression(bold("Copy")),
>> xlab=expression(bold("Stimulation")), main="Plot",
>> par.settings = list(strip.background=list(col="white")),
>> par.strip.text=list(font=2),
>> key = key.plot,
>> panel = function(x, y){
>> pnl = panel.number()
>> panel.abline(h = datmeA[datmeA[,2]==
>>
>> levels(datmeA[,2])[pnl],"ratio"], col = c("red","black"), lty=3)
>>
>> panel.stripplot(x,y, ...)
>> }
>> )
>>
>> On Sun, Apr 27, 2014 at 2:06 AM, Duncan Mackay <dulcalma at bigpond.com> wrote:
>>> Hi Luigi
>>>
>>> You are typing things unnecessarily: do not use the attach command unless
>>> absolutely necessary - it has unfortunate consequences.
>>> It is better to use with or within.
>>> alpha is not available with some devices with bad consequences if used; its
>>> default is 1 anyway.
>>>
>>> Once you have stated a data.frame as the data object it is usually not
>>> necessary to use the data.frame$ sign in to signify column names: use the
>>> column names.
>>> data = "a data.frame" is the equivalent to with
>>>
>>> You are reordering the levels of stimulation and changing the name of 1 so I
>>> thought it was easiest to make a column stim and do things there otherwise
>>> it the relevelling could be done in the data argument using the subset
>>> argument. Then the change to "Unst" could be done by using strip =
>>> strip.custom(factor.levels = ...),
>>>
>>> To change for the -/+ I made a group - the easiest way.
>>> Have a look a changing the negative symbol to 20 or something else as it is
>>> hard to visualise. You may vary things with changing cex (remember to have 2
>>> values 1 for each group).
>>>
>>> If you do str(xyplot object) you will get a big print of the object and
>>> within that the x limits are shown as "0", "1" which means that the x values
>>> are 1 and 2
>>> There is a command to get these things but I have forgotten it
>>>
>>> my.data$stimulation <- factor(levels = c("Unstimulated",
>>> "ESAT6","CFP10","Rv3615c","Rv2654", "Rv3879", "Rv3873","PHA"))
>>> my.data$stim <- factor(my.data$stimulation, labels = c("Unst.",
>>> "ESAT6","CFP10","Rv3615c","Rv2654", "Rv3879", "Rv3873","PHA"))
>>> my.data$pos <- ifelse(sign(my.data$copy) > 0, 2,1)
>>>
>>> stripplot(copy ~ factor(positivity)|stim,my.data,
>>> groups = pos,
>>> hor = F,
>>> layout = c(8,1),
>>> scales = list(x = list(at = c(1,2),
>>> labels = c("N","P"))),
>>> jitter.x = TRUE,
>>> amount = 2,
>>> pch = c(16,1),
>>> col = "black",
>>> ylab = expression(bold("Copy")),
>>> xlab = expression(bold("Stimulation")),
>>> main="Plot",
>>> par.settings = list(strip.background=list(col="white")),
>>> par.strip.text=list(font=2)
>>> )
>>>
>>> Regards
>>>
>>> Duncan
>>>
>>> Duncan Mackay
>>> Department of Agronomy and Soil Science
>>> University of New England
>>> Armidale NSW 2351
>>> Email: home: mackay at northnet.com.au
>>>
>>>
>>> -----Original Message-----
>>> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On
>>> Behalf Of Luigi Marongiu
>>> Sent: Sunday, 27 April 2014 02:07
>>> To: r-help at r-project.org
>>> Subject: [R] lattice plot formatting: pch, abbreviation and labels
>>>
>>> Dear all,
>>> I am trying to use the lattice plot, but the syntax is quite
>>> difficult. Specifically I have eight variables (1 to 8) each of them
>>> further subdivided in two classes (negative=0 and positive=1). I am
>>> using the stripplot() to represent these values. I would like to
>>> represent the negative and positive values with black and white dots
>>> so I have tried to use the argument pch=c(16, 1) both in the main
>>> stripplot function and embedded in the scale argument. However the
>>> resulting plot shows that some points are drawn with the pch=16 and
>>> other with pch=1 irrespective of their class.
>>> Is there a way to draw the values for the variable positivity = 0 with
>>> pch=16 and those with positivity = 1 with pch=0?
>>>
>>> In addition I would like to change the labels under the axis from 0,1
>>> to N,P. However when I placed labels=c("N", "P") or labels=list("N",
>>> "P") in the main stripplot() I did not obtained any difference and
>>> when placed within the scale argument also the -labels were modified.
>>> Is there a way to change the label 0 with N and the label 1 with P?
>>>
>>> final problem: I would like to abbreviate the "Unstimulated" box label
>>> with "Unst.". I have tried the abbreviate=TRUE argument but again the
>>> syntax is too complex for me and it did not work.
>>> Is there a way to abbreviate the variables names?
>>>
>>> Thank you very much for your help.
>>> Best wishes,
>>> Luigi
>>>
>>>
>>> CODE:::::::::
>>>
>>>
>>> ### open plot library
>>> library(lattice)
>>>
>>> my.data<-structure(list(
>>> column_1 = 1:120,
>>> column_2 = structure(c(
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8,
>>> 1,2,3,4,5,6,7,8), .Label = c("Unstimulated", "ESAT6", "CFP10",
>>> "Rv3615c", "Rv2654", "Rv3879", "Rv3873", "PHA"), class = "factor"),
>>> column_3 = structure(c(
>>> 0,0,0,0,0,0,0,0,
>>> 0,0,0,0,0,0,0,0,
>>> 0,0,0,0,0,0,0,0,
>>> 0,0,0,0,0,0,0,0,
>>> 0,0,0,0,0,0,0,0,
>>> 0,0,0,0,0,0,0,0,
>>> 0,0,0,0,0,0,0,0,
>>> 1,1,1,1,1,1,1,1,
>>> 1,1,1,1,1,1,1,1,
>>> 1,1,1,1,1,1,1,1,
>>> 1,1,1,1,1,1,1,1,
>>> 1,1,1,1,1,1,1,1,
>>> 1,1,1,1,1,1,1,1,
>>> 1,1,1,1,1,1,1,1,
>>> 0,0,0,0,0,0,0,0)),
>>> column_4 = c(
>>>
>>> 192.0519108,183.6403531,53.46798757,83.60638077,69.60749873,159.4706861,256.
>>> 8765622,499.2899303,
>>>
>>> 2170.799076,1411.349719,2759.472348,2098.973397,2164.739515,1288.676574,1611
>>> .486543,6205.229575,
>>>
>>> 870.7424981,465.9967135,191.8962375,864.0937485,2962.693675,1289.259137,2418
>>> .651212,7345.712517,
>>> 0,168.1198893,674.4342961,101.1575401,47.81596237,0,0,1420.793922,
>>>
>>> 142.6871331,5.466468742,291.9564635,80.73914133,73.02239621,64.47806871,144.
>>> 3543635,3167.959757,
>>>
>>> 3164.748333,1092.634557,28733.20269,1207.87783,729.6090973,151.8706088,241.2
>>> 466141,9600.963594,
>>>
>>> 1411.718287,12569.96285,1143.254476,6317.378481,16542.27718,79.68025792,1958
>>> .495138,7224.503437,
>>>
>>> 208.4382941,69.48609769,656.691151,0.499017582,7114.910926,187.6296174,41.73
>>> 980805,8930.784541,
>>>
>>> 4.276752185,0.432300363,60.89228665,1.103924786,0.490686366,1.812993239,7.26
>>> 4531581,1518.610307,
>>>
>>> 2172.051528,595.8513744,17141.84336,589.6565971,1340.287628,117.350942,593.7
>>> 034054,24043.61463,
>>>
>>> 0,81.83292179,1539.864321,36.41722958,8.385131047,161.7647376,65.21615696,72
>>> 65.573875,
>>>
>>> 97.84753179,154.051827,0.613835842,10.06138851,45.04879285,176.8284258,18795
>>> .75462,30676.769,
>>>
>>> 5780.34957,944.2200834,2398.235596,1083.393165,2541.714557,1251.670895,1547.
>>> 178549,1792.679176,
>>>
>>> 3067.988416,8117.210173,23676.02226,8251.937547,17360.80494,18563.61561,1694
>>> 1.865,31453.96708,
>>>
>>> 2767.493803,4796.33016,12292.93705,3864.657567,9380.673835,14886.44683,8457.
>>> 88646,26050.47191)),
>>> .Names = c("row", "stimulation", "positivity", "copy"), row.names =
>>> c(NA, -120L),
>>> class = "data.frame")
>>> attach(my.data)
>>>
>>> stripplot(my.data$copy ~
>>> factor(my.data$positivity)|factor(my.data$stimulation,
>>> levels = c("Unstimulated", "ESAT6","CFP10","Rv3615c",
>>> "Rv2654", "Rv3879", "Rv3873","PHA")),
>>> my.data, hor=F, layout = c(8,1), scales = list(relation =
>>> "same"),
>>> jitter.data=TRUE, alpha=1, pch=c(16,1), col="black",
>>> ylab=expression(bold("Copy")),
>>> xlab=expression(bold("Stimulation")), main="Plot",
>>> par.settings = list(strip.background=list(col="white")),
>>> par.strip.text=list(font=2))
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>
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